Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature.
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Molecular dynamics simulations were performed on a system consisting of a bilayer of 64 molecules of the lipid dipalmitoylphosphatidylcholine and 23 water molecules per lipid to reproduce the correct density and to give a proper estimate of the area per lipid.About:
This article is published in Biophysical Journal.The article was published on 1997-05-01 and is currently open access. It has received 1822 citations till now. The article focuses on the topics: Lipid bilayer phase behavior & Bilayer.read more
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GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
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Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
Jeffery B. Klauda,Richard M. Venable,J. Alfredo Freites,Joseph W. O’Connor,Douglas J. Tobias,Carlos Mondragon-Ramirez,Igor Vorobyov,Alexander D. MacKerell,Richard W. Pastor +8 more
TL;DR: The presented lipid FF is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.
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Structure of lipid bilayers
TL;DR: The uncertainty in structural results for lipid bilayers is being reduced and best current values are provided for bilayers of five lipids.
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Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets
Yusong Tu,Min Lv,Peng Xiu,Tien Huynh,Meng Zhang,Matteo Castelli,Z. Y. Liu,Qing（黄庆） Huang,Chunhai（樊春海） Fan,Haiping（方海平） Fang,Ruhong Zhou,Ruhong Zhou,Ruhong Zhou +12 more
TL;DR: Graphene nanosheets can penetrate into and extract large amounts of phospholipids from the cell membranes because of the strong dispersion interactions between graphene and lipid molecules as mentioned in this paper.
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Empirical force fields for biological macromolecules: overview and issues.
TL;DR: An overview of the issues associated with the development and application of empirical force fields to biomolecular systems and a summary of the force fields commonly applied to the different classes of biomolecules are presented.
References
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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
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A new force field for molecular mechanical simulation of nucleic acids and proteins
S. J. Weiner,Peter A. Kollman,David A. Case,U. C. Singh,Caterina Ghio,Giuliano Alagona,Salvatore Profeta,Paul K. Weiner +7 more
TL;DR: In this paper, a force field for simulation of nucleic acids and proteins is presented, which is based on the ECEPP, UNECEPP, and EPEN energy refinement software.
Book
Molecular theory of capillarity
John S. Rowlinson,B. Widom +1 more
TL;DR: The theory of Van Der Waals statistical mechanics of the liquid-gas surface model fluids in the mean-field approximation computer simulation of the calculation of the density profile three-phase equilibrium interfaces near critical points as mentioned in this paper.